Sediment bacterial assemblages inside and outside macrophyte beds in Yunnan Plateau lakes with contrasting nutrient levels and water depths

Eutrophication followed by deterioration of water quality and loss of aquatic plants is a global problem in aquatic ecosystems. Sediment microbial communities are often used as indicators of environmental changes due to their sensitive responses. However, the joint effects of nutrient levels and aquatic plants on the structure and function of bacterial assemblages remain unclear. In this study, four Yunnan Plateau lakes with contrasting nutrient levels were sampled in November 2021. Sediment samples were collected from areas with and without aquatic plants to explore the potential interactive effects of nutrients and plants. We found (1) that Lake Qilu had a significantly higher richness index than the other three lakes. Lake Lugu had the highest evenness variable among the four lakes. (2) PCoA showed strong clustering of bacterial communities according to nutrients, aquatic plants, and water depth. (3) A significant nutrient effect was also observed on bacterial function, as suggested by the increasing proportion of the five metabolic functions, including translation, ribosomal structure, and biogenesis, with increasing nutrient concentrations. (4) Nutrients explained 10.4% of the variation in bacterial communities, followed by plants (1.4%) and water depth (0.8%). Our findings suggest that eutrophication increased bacterial richness and affected key microbial taxa and functions.